AdapterRemovalSTAR 2.7.0d for visualisation and inspectionkallisto 0.43.1.
kallisto is able to proportionally assign multi-mapping readsGC content of each library showing uneven and ‘spikey’ patterns. Peaks on the RHS indicate potential incomplete rRNA removal, whilst the other indicate possible excessive PCR cycles and high levels of duplicated sequences.
STAR Alignment summary showing very low levels of unique alignments, which is again suggestive of incomplete rRNA removal. Uniquely mapping reads are now within the range usually seen after summarising to genes
After summarisation the library sizes ranged between 6,954,273 and 14,565,667
## Importance of components:
## PC1 PC2 PC3 PC4 PC5 PC6
## Standard deviation 69.5070 45.8828 28.5379 19.34833 15.64034 9.792e-14
## Proportion of Variance 0.5772 0.2515 0.0973 0.04473 0.02923 0.000e+00
## Cumulative Proportion 0.5772 0.8287 0.9261 0.97077 1.00000 1.000e+00
| ID | Name | logFC | AveExpr | t | P.Value | FDR | Location |
|---|---|---|---|---|---|---|---|
| ENSRNOG00000047551 | Pnpla2 | -7.193 | 0.1297 | -13.55 | 3.224e-06 | 0.02734 | 1:213997709-214002815:(+) |
| ENSRNOG00000050004 | LOC100909761 | 6.555 | -1.417 | 13.04 | 4.155e-06 | 0.02734 | 9:37727942-37747514:(+) |
| ENSRNOG00000032832 | Mmp10 | 3.502 | 2.164 | 9.505 | 3.31e-05 | 0.1411 | 8:5734348-5742243:(+) |
| ENSRNOG00000032626 | Mmp3 | 3.614 | 4.589 | 8.851 | 5.236e-05 | 0.1411 | 8:5676665-5698579:(+) |
| ENSRNOG00000002802 | Cxcl1 | 4.896 | 1.902 | 8.303 | 7.86e-05 | 0.1411 | 14:18743685-18745457:(-) |
| ENSRNOG00000010278 | Il6 | 4.791 | 0.1518 | 8.274 | 8.035e-05 | 0.1411 | 4:3043231-3047807:(+) |
| ENSRNOG00000007545 | Angptl4 | 1.852 | 3.859 | 8.232 | 8.3e-05 | 0.1411 | 7:18627808-18634079:(-) |
| ENSRNOG00000060849 | Rcor2 | -5.115 | -1.303 | -8.129 | 8.987e-05 | 0.1411 | 1:222519615-222524779:(+) |
| ENSRNOG00000000239 | Ccl7 | 2.753 | 2.899 | 8.037 | 9.652e-05 | 0.1411 | 10:69423086-69424979:(+) |
| ENSRNOG00000024705 | Rarres2 | 2.478 | 4.591 | 7.585 | 0.0001388 | 0.1548 | 4:78205812-78208767:(-) |
Genes to an FDR of 15.0%
Genes up to an FDR of 20%
R version 3.5.2 (2018-12-20)
**Platform:** x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C
attached base packages: stats4, parallel, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: ggrepel(v.0.8.0), plyranges(v.1.2.0), rtracklayer(v.1.42.2), GenomicRanges(v.1.34.0), GenomeInfoDb(v.1.18.2), IRanges(v.2.16.0), S4Vectors(v.0.20.1), scales(v.1.0.0), ngsReports(v.0.99.7), BiocGenerics(v.0.28.0), pander(v.0.6.3), magrittr(v.1.5), forcats(v.0.4.0), stringr(v.1.4.0), dplyr(v.0.8.0.1), purrr(v.0.3.2), readr(v.1.3.1), tidyr(v.0.8.3), tibble(v.2.1.1), ggplot2(v.3.1.0), tidyverse(v.1.2.1), edgeR(v.3.24.3) and limma(v.3.38.3)
loaded via a namespace (and not attached): nlme(v.3.1-137), bitops(v.1.0-6), matrixStats(v.0.54.0), lubridate(v.1.7.4), RColorBrewer(v.1.1-2), httr(v.1.4.0), tools(v.3.5.2), backports(v.1.1.3), R6(v.2.4.0), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), tidyselect(v.0.2.5), compiler(v.3.5.2), cli(v.1.1.0), rvest(v.0.3.2), Biobase(v.2.42.0), Cairo(v.1.5-9), xml2(v.1.2.0), DelayedArray(v.0.8.0), plotly(v.4.8.0), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.18), Rsamtools(v.1.34.1), rmarkdown(v.1.12), XVector(v.0.22.0), pkgconfig(v.2.0.2), htmltools(v.0.3.6), highr(v.0.8), htmlwidgets(v.1.3), rlang(v.0.3.2), readxl(v.1.3.1), rstudioapi(v.0.10), shiny(v.1.2.0), generics(v.0.0.2), zoo(v.1.8-5), hwriter(v.1.3.2), jsonlite(v.1.6), crosstalk(v.1.0.0), BiocParallel(v.1.16.6), RCurl(v.1.95-4.12), GenomeInfoDbData(v.1.2.0), Matrix(v.1.2-17), Rhdf5lib(v.1.4.3), Rcpp(v.1.0.1), munsell(v.0.5.0), stringi(v.1.4.3), yaml(v.2.2.0), MASS(v.7.3-51.1), SummarizedExperiment(v.1.12.0), zlibbioc(v.1.28.0), rhdf5(v.2.26.2), plyr(v.1.8.4), grid(v.3.5.2), promises(v.1.0.1), crayon(v.1.3.4), lattice(v.0.20-38), Biostrings(v.2.50.2), haven(v.2.1.0), hms(v.0.4.2), locfit(v.1.5-9.1), knitr(v.1.22), pillar(v.1.3.1), XML(v.3.98-1.19), glue(v.1.3.1), evaluate(v.0.13), ShortRead(v.1.40.0), latticeExtra(v.0.6-28), data.table(v.1.12.0), modelr(v.0.1.4), httpuv(v.1.5.0), cellranger(v.1.1.0), gtable(v.0.3.0), assertthat(v.0.2.1), xfun(v.0.5), mime(v.0.6), xtable(v.1.8-3), broom(v.0.5.1), later(v.0.8.0), viridisLite(v.0.3.0), truncnorm(v.1.0-8) and GenomicAlignments(v.1.18.1)